Application of Proteomics and Metabolomics in Interstitial Lung Disease Research
Keywords:
Interstitial lung disease, Proteomics, Metabolomics, Disease biomarkers, Pathogenesis, Metabolic pathwaysAbstract
Interstitial lung disease (ILD) is a heterogeneous group of disorders characterized by pathological changes such as inflammatory infiltration, fibrosis, and cell proliferation involving the lung interstitium. The clinical etiology of this disease is not yet fully understood, especially during acute exacerbations, where patients often have a poor prognosis. The combined use of proteomics and metabolomics holds promise as a powerful tool for screening novel biomarkers of ILD. This article reviews the application of proteomics and metabolomics techniques in the study of ILD, aiming to clarify the current research status and provide an outlook for future research directions.
References
Lederer DJ, Martinez FJ, 2018, Idiopathic Pulmonary Fibrosis. N Engl J Med, 378(19): 1811–1823.
Poletti V, Egan J, 2013, Classification, Natural History, and Staging of Idiopathic Pulmonary Fibrosis. Sarcoidosis Vasc Diffuse Lung Dis, 30(Suppl 1): 13–20.
Collard HI, Ryerson CJ, Corte TJ, et al., 2016, Acute Exacerbation of Idiopathic Pulmonary Fibrosis: An International Working Group Report. Am J Respir Crit Care Med, 194(3): 265–275.
Farrand E, Vittinghoff E, Ley B, et al., 2020, Corticosteroid Use is Not Associated with Improved Outcomes in Acute Exacerbation of IPF. Respirology, 25(6): 629–635.
Salonen J, Purokivi M, Bloigu R, et al., 2020, Prognosis and Causes of Death of Patients with Acute Exacerbation of Fibrosing Interstitial Lung Diseases. BMJ Open Respir Res, 7(1): e000563.
Yu G, Ibarra GH, Kaminski N, 2018, Fibrosis: Lessons from OMICS Analyses of the Human Lung. Matrix Biol, (68–69): 422–434.
Dubin RF, Rhee EP, 2020, Proteomics and Metabolomics in Kidney Disease, Including Insights into Etiology, Treatment, and Prevention. Clin J Am Soc Nephrol, 15(3): 404–411.
Deberardinis RJ, Keshari KR, 2022, Metabolic Analysis as a Driver for Discovery, Diagnosis, and Therapy. Cell, 185(15): 2678–2689.
Wu Y, Li Y, Luo Y, et al., 2023, Proteomics: Potential Techniques for Discovering the Pathogenesis of Connective Tissue Diseases—Interstitial Lung Disease. Front Immunol, (14): 1146904.
Rozanova S, Barkovits K, Nikolov M, et al., 2021, Quantitative Mass Spectrometry-Based Proteomics: An Overview. Methods Mol Biol, (2228): 85–116.
Foster MW, Morrison LD, Todd JL, et al., 2015, Quantitative Proteomics of Bronchoalveolar Lavage Fluid in Idiopathic Pulmonary Fibrosis. J Proteome Res, 14(2): 1238–1249.
Haggmark A, Hamsten C, Wiklundh E, et al., 2015, Proteomic Profiling Reveals Autoimmune Targets in Sarcoidosis. Am J Respir Crit Care Med, 191(5): 574–583.
Kjellin H, Silva E, Branca RM, et al., 2016, Alterations in the Membrane-Associated Proteome Fraction of Alveolar Macrophages in Sarcoidosis. Sarcoidosis Vasc Diffuse Lung Dis, 33(1): 17–28.
O’Dwyer DN, Norman KC, Xia M, et al., 2017, The Peripheral Blood Proteome Signature of Idiopathic Pulmonary Fibrosis is Distinct from Normal and is Associated with Novel Immunological Processes. Sci Rep, (7): 46560.
Ahrman E, Hallgren O, Malmstrom L, et al., 2018, Quantitative Proteomic Characterization of the Lung Extracellular Matrix in Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. J Proteomics, (189): 23–33.
Moodley YP, Corte TJ, Oliver BG, et al., 2019, Analysis by Proteomics Reveals Unique Circulatory Proteins in Idiopathic Pulmonary Fibrosis. Respirology, 24(11): 1111–1114.
Tian Y, Li H, Gao Y, et al., 2019, Quantitative Proteomic Characterization of Lung Tissue in Idiopathic Pulmonary Fibrosis. Clin Proteomics, (16): 6.
Todd JL, Neely ML, Overton R, et al., 2019, Peripheral Blood Proteomic Profiling of Idiopathic Pulmonary Fibrosis Biomarkers in the Multicentre IPF-PRO Registry. Respir Res, 20(1): 227.
Carleo A, Landi C, Prasse A, et al., 2020, Proteomic Characterization of Idiopathic Pulmonary Fibrosis Patients: Stable Versus Acute Exacerbation. Monaldi Arch Chest Dis, 90(2): 180.
Moodley Y, 2020, In Search for a Predictive Marker of Acute Exacerbations of Idiopathic Pulmonary Fibrosis. Respirology, 25(3): 234–235.
Majewski S, Zhou X, Milkowska-Dymanowska J, et al., 2021, Proteomic Profiling of Peripheral Blood and Bronchoalveolar Lavage Fluid in Interstitial Lung Diseases: An Explorative Study. ERJ Open Res, 7(1): 00489–2020.
Sivakumar P, Ammar R, Thompson JI, et al., 2021, Integrated Plasma Proteomics and Lung Transcriptomics Reveal Novel Biomarkers in Idiopathic Pulmonary Fibrosis. Respir Res, 22(1): 273.
Bowman WS, Newton CA, Linderholm AL, et al., 2022, Proteomic Biomarkers of Progressive Fibrosing Interstitial Lung Disease: A Multicentre Cohort Analysis. Lancet Respir Med, 10(6): 593–602.
Matson SM, Lee JS, 2022, In Search of the Elusive Biomarker(s): A Proteomics Analysis in Rheumatoid Arthritis-Associated Interstitial Lung Disease. Thorax, (10): 949.
Wu X, Jeong Y, Poli de Frias S, et al., 2022, Serum Proteomic Profiling of Rheumatoid Arthritis-Interstitial Lung Disease with a Comparison to Idiopathic Pulmonary Fibrosis. Thorax, (10): 1031–1044.
Hanash S, 2003, Disease proteomics. Nature, 422(6928): 226–232.
Saraswat M, Joenvaara S, Tohmola T, et al., 2020, Label-Free Plasma Proteomics Identifies Haptoglobin-Related Protein as Candidate Marker of Idiopathic Pulmonary Fibrosis and Dysregulation of Complement and Oxidative Pathways. Sci Rep, 10(1): 7787.
Yamaguchi K, Iwamoto H, Sakamoto S, et al., 2020, Serum High-Mobility Group Box 1 is Associated with the Onset and Severity of Acute Exacerbation of Idiopathic Pulmonary Fibrosis. Respirology, 25(3): 275–280.
Chen G, Deutsch GH, Schulert GS, et al., 2022, Identification of Distinct Inflammatory Programs and Biomarkers in Systemic Juvenile Idiopathic Arthritis and Related Lung Disease by Serum Proteome Analysis. Arthritis Rheumatol, 74(7): 1271–1283.
Rinschen MM, Ivanisevic J, Giera M, et al., 2019, Identification of Bioactive Metabolites Using Activity Metabolomics. Nat Rev Mol Cell Biol, 20(6): 353–367.
Johnson CH, Ivanisevic J, Siuzdak G, 2016, Metabolomics: Beyond Biomarkers and Towards Mechanisms. Nature Reviews Molecular Cell Biology, 17(7): 451–459.
Xie N, Tan Z, Banerjee S, et al., 2015, Glycolytic Reprogramming in Myofibroblast Differentiation and Lung Fibrosis. American Journal of Respiratory and Critical Care Medicine, 192(12): 1462–1474.
Kang YP, Lee SB, Lee JM, et al., 2016, Metabolic Profiling Regarding Pathogenesis of Idiopathic Pulmonary Fibrosis. Journal of Proteome Research, 15(5): 1717–1724.
Yan F, Wen Z, Wang R, et al., 2017, Identification of the Lipid Biomarkers from Plasma in Idiopathic Pulmonary Fibrosis by Lipidomics. BMC Pulmonary Medicine, 17(1): 174.
Zhao YD, Yin L, Archer S, et al., 2017, Metabolic Heterogeneity of Idiopathic Pulmonary Fibrosis: A Metabolomic Study. BMJ Open Respiratory Research, 4(1): e000183.
Rindlisbacher B, Schmid C, Geiser T, et al., 2018, Serum Metabolic Profiling Identified a Distinct Metabolic Signature in Patients with Idiopathic Pulmonary Fibrosis—A Potential Biomarker Role for LysoPC. Respiratory Research, 19(1): 7.
Gaugg MT, Engler A, Bregy L, et al., 2019, Molecular Breath Analysis Supports Altered Amino Acid Metabolism in Idiopathic Pulmonary Fibrosis. Respirology, 24(5): 437–444.
Kim HS, Yoo HJ, Lee KM, et al., 2021, Stearic Acid Attenuates Profibrotic Signaling in Idiopathic Pulmonary Fibrosis. Respirology, 26(3): 255–263.
Nambiar S, Clynick B, How BS, et al., 2021, There is Detectable Variation in the Lipidomic Profile Between Stable and Progressive Patients with Idiopathic Pulmonary Fibrosis (IPF). Respiratory Research, 22(1): 105.
Nambiar S, Tan DBA, Clynick B, et al., 2021, Untargeted Metabolomics of Human Plasma Reveal Lipid Markers Unique to Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Proteomics Clinical Applications, 15(2–3): e2000039.
Gao S, Li X, Jiang Q, et al., 2022, PKM2 Promotes Pulmonary Fibrosis by Stabilizing TGF-β1 Receptor I and Enhancing TGF-β1 Signaling. Science Advances, 8(38): eabo0987.
Vietri L, Bennett D, Cameli P, et al., 2019, Serum Amyloid A in Patients with Idiopathic Pulmonary Fibrosis. Respiratory Investigation, 57(5): 430–434.
Vietri L, D’Alessandro M, Bergantini L, et al., 2020, Specificity of Serum Amyloid A as a Biomarker of Idiopathic Pulmonary Fibrosis. Internal Medicine Journal, 50(12): 1571–1574.
Yang J, Chen C, Chen W, et al., 2021, Proteomics and Metabolomics Analyses of COVID-19 Complications in Patients with Pulmonary Fibrosis. Scientific Reports, 11(1): 14601.
Mirsaeidi M, Banoei MM, Nienow CK, et al., 2016, Plasma Metabolomic Profile in Fibrosing Pulmonary Sarcoidosis. Sarcoidosis Vasculitis and Diffuse Lung Diseases, 33(1): 29–38.
Dasgupta S, Ghosh N, Choudhury P, et al., 2022, NMR Metabolomic and Microarray-Based Transcriptomic Data Integration Identifies Unique Molecular Signatures of Hypersensitivity Pneumonitis. Molecular Omics, 18(2): 101–111.